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sciencehabit writes "The carnivorous humped bladderwort, found on all continents except Antarctica, is a model of ruthless genetic efficiency. Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene. The bladderwort, named for its water-filled bladders that suck in unsuspecting prey, is a relative of the tomato. The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life."

The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life.

False. Unsurprisingly, nowhere in the paper was this dubious claim even approached. Instead you can find this even in the summary:

However, extreme genome size reductions have been reported in the angiosperm family tree.

Emphasis mine. And then further into the actual paper:

Relaxed selection pressure for unnecessary functions probably led to gene losses, whereas in other cases, gene family expansions may have been promoted by selection. Evidence for localized selection on the U. gibba gene complement, however, does not provide support for the existence of genome-wide selective forces that might favour reduction of nonessential, non-coding DNA.

I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.

We can tell the composition of the junk for approximately 66% of the human genome. There is a small amount of regulatory elements mixed with all this junk, but the junk itself is not necessary for anything.

Even without the extreme examples such as bladderwort we readily observe 10x variability in the amount of DNA between fairly recently separated species.

Um, where do you get those numbers? At least 76% of the non-coding human genome is transcribed [sciencemag.org] -- to what end we cannot be certain in all cases, but the RNA transcripts from these often are fed back into gene expression and regulation. It's estimated that well over 50% of non-coding DNA is heavily conserved by evolutionary processes and contributes significantly to fitness.

My reading of those critiques was that because someone could not describe the purpose of this DNA, it was "junk," despite the fact that the DNA was getting transcribed and was having biochemical interaction in the cell. I think the "conservatives," or the ones how think there's a lot of junk, are thinking teleologically about the "purpose" of DNA and are simply excluding these other sequences because the cannot give a complete account of their purpose or whatever advantage they may confer to the phenotype.

Again, we CAN describe the function of about 70% of junk - it simply wants to replicate itself as much as possible. Google for "retrotransposons". Non-junk actually _has_ a purpose - it's used to encode the cell functions.

Take a deep breath, and say to yourself less than one percent of junk DNA has biological activity in the cell. Unless, of course, you use ENCODE's physical chemistry definition of biological activity. One of the definitions of biological activity ENCODE used was "is transcribed", even when the transcribed RNA is then immediately discarded. Note that junk DNA tends to be copied in one copy number, but the mRNA it is supposed to control by binding tends to have copy numbers in the thousands (the small amount

Junk for an individual. Not necessarily junk for the evolution of a species. This issue comes up in computer science too with genetic algorithms, pushing pressure to keep the encoding as compact as possible 'may' lead to the side effect of increasing the probability of being stuck on a local optima. There's a lot of math 'n stuff involved that can better be explained by experts, but here's the short version: let's say that a genetic algorithm engine has an individual settled for a local optimum with all the bits just right. But there's a possible mutation that could lead to finding a slope leading to a better optimum. Obviously there's the issue that the mutation is going to compromise something important, and you end up with a mutant with good potential but a weaker fitness score, so the mutation is more likely to be discarded. However, if there's non-functional bits in the individual, there's a higher chance that the mutant can score better by compromising something that wasn't in use to being with, hence non-functional coding genes having some use in the long run. Now this is a huge simplification on a complex matter, but this does come up.

I'm extremely familiar with genetic algorithms. Pure junk is generally useless because you're no better off than starting from scratch. You need at least something that is _almost_ junk or a way to create imperfect copies of existing functional elements within a genome.

Unsurprisingly, there are mechanism for both of these. And they don't need junk DNA - bacteria can evolve just fine and they have virtually no junk DNA.

Then the question: "why junk DNA?" and the answer so far is that it has negligible f

Technically speaking, my line of work was with linear genetic programming as opposed to vanilla GAs, but disallowing or penalizing fitness scores based on having non-functional code can easily slow convergence. I'm focused more on the math/statistics side than coding side, but for our cases our calculated expected value of beneficial point mutations was higher when non-functional operands were permitted. Negative, but still better than for equivalent individuals with removed junk.

Next question: "Then why does this plant has so little junk?". That's probably because it has some rogue transposable element that chews portions of DNA randomly.

??? This is generally NOT the mechanism behind massive genome reductions

I'm not the one you're responding to, but as a curiosity, what is the mechanism behind genome reductions?What kind of copying errors decrease the size of the DNA chain and how probable they are compared to block copies etc., which increase it.

What's with the "junk" theorizing about "junk" being "not necessarily junk" for evolution? And the "junk" assumption that the "junk" need be explained in terms of evolutionary dependence on "junk"? The "junk" in the human genome has been mentioned, http://science.slashdot.org/comments.pl?sid=3745175&cid=43712851 [slashdot.org], to contain segments with products for transcription etc., e.g. the ribosome is a ton of RNA (plus proteins), (and the other molecular factory machinery/parts aren't all proteins, but include a

First off, I am a math guy, not a science guy. I have never pursued a grant for anything evolution related, so don't complain at me about it. Don't whine at a fireman for making a mediocre cop. And pay bloody attention to what you reply to, my post was about the issue (whether or not junk DNA being useless) also appearing in computer science.

Second, major logic fallacy and incorrect use of basic terms right off the bat

What's with the "junk" theorizing about "junk" being "not necessarily junk" for evolution

I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.

As a biologist and software developer, I have a hard time understanding what you are trying to say here.

Indeed, repetitive heterochromatin (that which is called junk DNA) is found at centromeres [wikipedia.org] which are where sister chromatids are held together. Centromeres are essential for mitosis and meiosis in most macroscopic species, certainly plants and humans. And I think the consensus is that if you don't have "junk DNA" sequences for the centromere, the centromere will pick a place on the chromosome to form, and that area will become junk DNA even if it's not meant to be. So you will always have "junk DNA" if y

This pissed me off so much I just registered FactCheckScience.org
Currently finishing PhD thesis writing (bioinformatics) so I dont have time to invest in a domain.
If anyone has a stellar idea, I'm an Open Source supporter and happy to share the domain.
This has to stop.

My understanding is that junk DNA is no longer a useful term because the DNA that isn't translated has been found to have structural and other epigenetic properties. I wonder if the complexity of mamallian vs. plant development plays a role here. Any biologists out there?

Not all untranslated DNA has other properties. Some of it really does just exist because it's good at getting itself replicated. It's an open question how much non-coding DNA exerts regulatory effects and how much is actually junk. This paper indicates that in at least one eukaryote, 3% non-coding DNA is sufficient to regulate all the coding DNA.

If that holds in mammals (unlikely, but not out of the question), the vast majority of our non-coding DNA would still be "junk". Human DNA is 98% non-coding, or 2% coding. 3% of 2% is a rounding error here, so it would still be accurate to say the human genome is 98% "junk". If regulatory sequences outnumbered coding sequences 10:1 you're still looking at >75% of the human genome being "junk".

I don't think the concept of "junk" DNA is ever going to go away. Evolution would predict that sequences that are good at replicating themselves would accumulate in the genome, even if they don't do anything "useful". And random errors that accrue during copying will persist unless there's a mechanism to select against them. If we found that 100% of our DNA had a purpose, that would be a pretty strong argument against the theory of evolution.

The interesting question here is what selective forces drive this plant to excise unnecessary DNA, and what mechanism it uses to do this. Understanding that mechanism might lead to future gene therapies.

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene? Is it actually handy to have these around to allow for rapid bigger changes of set of active genes than just a few small mutations in the active genes can do?
It would seem that almost all such massive additions to what's active would be deleterious, but maybe they provide a safeguard against rapid change of environment.
So how far off from "being coding" are these junk re

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene? Is it actually handy to have these around to allow for rapid bigger changes of set of active genes than just a few small mutations in the active genes can do?

That why they are called junk DNA and not trash DNA, because at least part of it is ready to be reused later.

Some parts will be to control which genes are actually activated, some might even only be necessary to determine how the DNA is folded to determine what genes get more exposure, but the thousends of broken and useless copies of genes around in the junk DNA surely also have the function of collecting mutations until they might get by chance to something useful one day.

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene?

I have heard this suggestion before. One of my professors in fact mentioned that he's a bit nervous when getting vaccines because there's a chance some bit of retrovirus which incorporated into the genome millions of years ago might combine with the non-virulent vaccine to make a supervirus.

I'd estimate the chances of that happening are in the same ballpark as two seperate meteorites simultaneously smacking into your head from opposites sides, smooshing your brain out of your nose, so don't skip the vac

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene?

Yes! Even if the junk DNA doesn't serve a functional purpose in an organism, keeping it around can increase genetic diversity and potentially increase the adaptability of the species as a whole. Many of our functional coding genes have incomplete copies known as pseudogenes stuck in random places in the genome. It is possible for these genes to get reactivated with the ri

I don't think the concept of "junk" DNA is ever going to go away. Evolution would predict that sequences that are good at replicating themselves would accumulate in the genome, even if they don't do anything "useful".

No, no it wouldn't. I am a fan of taking simple logic like that and concluding "it must be in play", but there are other equally valid pieces of simple logic that it must compete (or be in equilibrium) with. One of those off the top of my head: Evolution would predict that an excess of junk DN

Evolution would predict that an excess of junk DNA would be detrimental to the organism since the likelihood of a random mutation turning some of that junk into something harmful goes up with the amount of junk.

But wouldn't evolution also predict that the junk DNA would stick around, because the multitude of random changes necessary to get rid of the junk DNA would have to confer other benefits, so as to give positive reinforcement for its survival?

But wouldn't evolution also predict that the junk DNA would stick around, because the multitude of random changes necessary to get rid of the junk DNA would have to confer other benefits, so as to give positive reinforcement for its survival?

Not necessarily. As long as the random changes are not contra-survival, there would be no particular impetus one way or the other.

You're right, but what is the positive reinforcement for the removal of the junk DNA then? It seems to me like the "more junk DNA means more places for an error" effect would be dwarfed by the "general" positive/negative mutation process... Heck, isn't it possible for the junk DNA to mutate into being NON-junk? (Which I guess is what a mutation that causes cancer would be.)

You're right, but what is the positive reinforcement for the removal of the junk DNA then? It seems to me like the "more junk DNA means more places for an error" effect would be dwarfed by the "general" positive/negative mutation process... Heck, isn't it possible for the junk DNA to mutate into being NON-junk? (Which I guess is what a mutation that causes cancer would be.)

Yes, but consider, that if there is going to be an error, would you want it happening in essential DNA, or in junk DNA that doesn't do anything anyway? Sometimes hiding your tree in a forest is a good thing.

In this specific case, my guess as a biotechnologist would be Nitrogen starvation. Carnivorous plants live in nitrogen poor areas, they only get nitrogen from the insects they catch. DNA replication requires quite a bit of nitrogen, so less DNA means the plant needs less nitrogen to copy a cell.

You also have to balance in the safety that this offers, in regard to random gene insertions from virus infections.

In a "clean" genome, these random insertions can break biologically critical genes. With a large "junk" store, the injection and integration of the virus has a much lower chance of disrupting a vital cellular mechanism.

Your science is dated. That old thought about DNA having a ton of junk was based on an absence of evidence: there was on the one hand "the central dogma" (that actual term used in science and, as my genetics professor put it, still about the best had) that DNA-->RNA-->protein, and thus it was assumed we could cause transcription in a tube and if no protein resulted, it was assumed "it must be junk; evolution demands it!!!" But then animals started dying when experimental gene therapies targeted "junk"

It's like this: If you have a big enough ego, everything you don't understand must be unimportant junk.

Putting this in perspective with the traditional slashdot car analogy: all parts of your car that are not also part of a bicycle are just junk. This bladderwort's a bicycle, a honey badger is a car, see?

If you have a big enough ego, everything you don't understand must be unimportant junk.

I think people read too much into the use of the word "junk", and attribute a pejorative meaning that wasn't necessarily intended. The best explanation I've seen (can't remember the source, sorry) was something along the lines of "junk is the stuff I keep in my attic; stuff I throw out is garbage." Biologists are in fact aware that non-coding parts of the genome can be essential, and there was never any presumption that anything we didn't understand was unimportant - however, how much of the non-coding DNA is genuinely necessary is an open question, and it's hard to find an obvious use for most of it. Clearly some complex organisms get along fine without it, so it's not unreasonable to view junk DNA primarily as a side effect of millions of years of evolution.

I dunno. When I was having this argument 20 years ago all the geneticists I was working with at the time were insisting that "junk DNA" was literally leftovers with no purpose.

As an information scientist, though, I knew this had to be incorrect. Absent a really strongly supported, well understood mechanism it's illogical to suppose that natural selection would overwhelmingly favor massive storage abuse. It's more reasonable to suppose that there's something going on that's completely off the radar. Reme

It's only evolution works just the other side around. Absent a really strongly unfitting characteristic of the junk DNA, it's not going to go anywhere. And, as an information scientist you already have the tools to discriminate one from the other: random wandering. You expect higher stability on pieces of DNA that do something useful than on tho

Your logic seems circular to me. You've stated the conclusion as a premise ("evolution works just the other side around") and you've used your definition of what you expect to happen as the means of evaluating what has happened ("do something useful" = "the only function of DNA we have so far discovered"). It's not possible to repeatably test your argument; so even if it's correct it's not really science, it's philosophy (or possibly religion).

"You've stated the conclusion as a premise ("evolution works just the other side around")"

Nope. I didn't set conclusion as premise, evolution *does* in fact works the other way around, it is a premise (under this conversation constrains): random mutations happen all the time, if they produce a better fit, they get selected by means of higher offspring, if they are deletereal they get off the pool and if they are neutral, they simply accumulate. It's believed -and supported by experimentation, that random

I guess we'll have to disagree since our arguments have conflicting premises.

1) You are still not giving up your definition of "functional" which I still contend is circular reasoning.

2) You've characterized my argument as an anthropomorphization of nature which is not my intent at all. I am merely refusing to accept a dubious categorization. The burden of proof is on those who would make this categorization, and I find their arguments very unconvincing.

As Hatta explained, some parts of gnomes really are useless, others code for genes and others provide structure. And indeed this chaos displays the lack of foresight evident in organically evolved systems. The word "junk" not a problem unless you want to argue that every gene in all genomes is there according to some intelligent design, which of course, it's what members of the Abrahamic religions are so desperate to pass for science.

This demonstrates only that organisms with little junk DNA can exist. To really demonstrate that "junk DNA" does nothing, someone needs to take an organism that has lots of junk DNA, sequence it, replace all the junk with the DNA equivalent of nulls, synthesize the new DNA, grow a new organism, and produce a few generations of it. Good project for Craig Venter.

There's a suspicion that "junk DNA", while currently turned off, sometimes gets turned on when mutation flips a bit, and this helps evolution along. An organism with little or no junk DNA may not evolve further, but can exist and reproduce just fine.

someone needs to take an organism that has lots of junk DNA, sequence it, replace all the junk with the DNA equivalent of nulls, synthesize the new DNA, grow a new organism, and produce a few generations of it. Good project for Craig Venter.

No need for Venter, nature has already done this experiment for us. Single Nucleotide Polymorphisms, or snips, occur in the human genome by the tens of millions. When a snip occurs inside a gene, it can have an effect such as increased incidence of a disease. Also snips in gene control regions can effect phenotype. But for the junk DNA, the tens of millions of random junk snips you and I have different, they just don't seem to have any effect whatsoever. If the code sequences in the junk matter, the effect

Also snips in gene control regions can effect phenotype. But for the junk DNA, the tens of millions of random junk snips you and I have different, they just don't seem to have any effect whatsoever. If the code sequences in the junk matter, the effect on the individual seems to be very slight.

Except for, you know, all the SNPs in noncoding regions which come up as significant in practically every GWAS ever.

It was thought the the PNA is just a junk "addition", but recently, SURPRISE, it was found out that it is even more important than DNA, in some aspects of course...
Or with other words, NO, i will not give up my junk DNA, it is mine. Period.

I note that the little digital clock on my desk does not need a 1TB disk drive full of software in order to operate either.

Constructing a large mammalian brain complete with things like "instincts" might well make use of non-protein-coding information of some sort.

One thing about biology and the functioning of cells that you learn pretty quick is that "if it can happen then it probably does", and this is a very strong argument against writing off anything that appears to be conserved as "useless".

Simply finding an organism that itself has no need of other information simply says that it's not a universal requirement, and doesn't really tell you anything about whether other organisms might have found a use for it.

So, this is offtopic but I thought humped bladderwort was a pretty unfortunate name. However a Google search and a couple of clicks later I land on the broom-rape cancer-root [usda.gov], of which there is an alpine, a Mexican, and an American variety.

A quick google reveals that phosphorus is about 1/10th of the total mass of DNA.Or, for an 80Mbase pair genome, about 160M atoms of phosphorus per cell.Randomly assuming the cells are 10um in size, and cubic leads to a volume of 10^-15m^3, or a mass of 10^-15 tons ish.10^-9 grams.Working out the mass of potassium in DNA comes out to 10^-15 grams.

Or around one ppm, perhaps 20 if considering only dry matter.

This would seem to indicate my initial thought it might be due to elemental phosphorous deficiency maki

Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene.... The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life.

What's so difficult to understand? Obviously, when it actually finds itself in need of some junk DNA, it just eats up a few people. Isn't this called Just-in-Time in business management?

As we learn how DNA is used to create RNA, mRNA, siRNA, miRNA, circRNA, microRNA, etc - by folding, spindling, adapting to environmental messages and signals, we find that a lot of what you think is "junk" DNA is in fact... NOT.

Some is, of course, but the conclusion is... WRONG. Most of the actual junk is actually viral rewrites (true junk), but a lot of the other stuff is boostrap shifted code designed to handle various conditions that may or may not be present.

For example, if you take a drug that shuts down a primary biochemical pathway, the cells turn on a second biochemical pathway - which may or may not be optimized. If the secondary biochemical pathway is shut down by drugs or damage, a tertiary - conserved, usually evolutionarily conserved fallback from when you were a fish or ratlike creature - kicks in.

You think it's junk. It's just code that turns on when you mess with the program or force certain conditions to occur.

"usually evolutionarily conserved fallback from when you were a fish or ratlike creature - kicks in."

There is no reason to believe that natural selection will preserve unused gens so long. Random mutation would have likely destroyed the genes a long time ago without any selective pressure to preserve them. There is absolutely no evidence to suggest that we all share a common ancestor. I know these views are unpopular around here but it doesn't make them any less valid.

Oh, silly silly anti-evolutionist. Tell that to your fuel-producing mitochondrial DNA that we stole millions of years ago and inherit from our mothers.

That claim is seriously misleading. According to Wikipedia, the closest connection between the bladderwort and the tomato seems to be that both are asterids of clade euasterids I. As are all other solanaceae besides tomatos (e.g. potatos, tobacco, petunias), all other lamiales besides bladderwort (e.g. acanthus, olives, plantains - the little green plants not the bananas, verbena) and many other plants such as forget-me-nots or gentiana. Initially they even got the time of the evolutionary split wrong by a factor of 1000!

I guess the truth is that the tomato genome is exceptionally well known and the two species are close enough to make a comparison reasonable. And to quote from the actual original article's abstract: "Unexpectedly, we identified at least three rounds of WGD [whole genome duplication] in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis)."

Second author on the paper here and the person who did the analyses that lead the the conclusion of three WGDs since divergence with tomato. We had to phrase the claim like that because tomato was the closest relative with a published genome. These analyses would have been a lot easier if there were genome sequences of plants more closely related to Utricularia, especially if some had more shared WGDs.

Obviously you (the authors) are not to blame for this. In the original article everything was in the proper context. But the author of the report in Science should have explained what bladderworts are like and instead ran away with a misunderstood bit of information ripped out of context. *This* is what provoked comments such as "Where pray tell then are the GM tomatoes that eat aphids?" and references to killer tomatos. (Of course, otherwise we might have been speculating instead on how many of you gave th

junk. I mean I look at it like this. When I upgrade to a new computer I copy the entire contents of my hard drive to the new bigger one.(Since that's the easiest thing to do. I don't have to figure out what's my data and what's not. Just plug it in and tell my new computer to copy everything and come back hours later.) Admittedly a lot of the stuff I'm copying over are OS files and installed programs. I always tell myself to go back and clean that stuff out but I never do since that'd take time and effort a

There is a difference between useful and necessary. Backups, for example, can be useful when you need them but they aren't necessary for your computer to function. Lots of genes maybe dormant and only activated when needed or they may perform useful functions but that's not to say what they do is absolutely necessary in all conditions. The cost of duplicating a gene must be weighed with the degree it benefits the organism in a particular environment.